The Flare Storm
by Mad3line
Summary: What if Thomas wasn’t immune and had the flare? What if WICKED wasn’t lying to the Gladers that he had become violent? Thomas begins to feel the insanity creep in when he begins to smell. Bad.
1. chapter 1

A/N: Hi! This is my second fanfic ever so it might not be that good. There's many Death Cure spoilers and is based off the books. But it's about Thomas who ends up catching the flare and not being immune instead of Newt. A lot of the story is based on James Dashner's book, Death Cure.

Disclaimer: I'm not James Dashner (as you may of guessed) and all of these characters are his, not mine along with the main plot.

Hope you like it, enjoy!

It was the smell that began to drive Thomas slightly mad. Not being alone for a few weeks. Not the blinding white walls, ceiling and floor. Not the lack of windows or the fact that they never turned off the lights. None of that. They'd taken his watch; they fed him the same exact shucking meal three times a day -- never spoke to him, never allowed anyone else in the room. No books, movies or games. Although this was WICKED Thomas was dealing with, he'd expected a little more.

With complete isolation, Thomas found himself growing angrier and angrier by the second. When he was first thrown into this useless place, there was only a toilet and an old wooden desk that Thomas couldn't reach, surrounded by an invisible barrier. With no bed or blanket, he found himself huddled up in a corner when night came, or at least what he assumed was night, having his watch taken away and all.

The unbearable time spent isolated left Thomas alone with his own thoughts, which had strayed to the worst ideas that had happened to his friends. But most of the time Thomas thought about the disease rooted inside him: the Flare, that silent, creeping virus that slowly took away everything that made a person human.

None of this drove him crazy.

But by the second week, he stank. For some reason, that set his nerves on a sharp wire, cutting into the solid block of his sanity. He wasn't allowed to shower or bathe, nor had he been provided a fresh set of clothes since the Scorch. Although he had asked multiple times for a rag to the hand pushing the food to Thomas, they never complied. Thomas settled for pouring some of his drinking water on his shirt which didn't even dent the frightful smell.

The deteriorating hygiene pushed against his mind, causing him to feel as though he lost it. Horrific thoughts seeped into his mind, like he was rotting, decomposing, his insides turning as rancid as his outside felt. Thomas began to believe that this unceasing stench represented death itself, rushing in, about to swallow him whole.

Those dark thoughts began to make him wonder if Teresa hadn't been lying to him the last time they spoke, when she said he had become crazy and violent. Unless while he was knocked out, Thomas had never believed he had done such things but now, maybe, just maybe she was correct.

With those ideas, rage seeped it's way in and Thomas found himself shaking uncontrollably at times, unable to control the fury. At first, Thomas thought this was just a result of being kept in a cramped room for so long. But around what Thomas guessed the third week, he began to scratch himself, losing control of what he was doing for up to an hour. When the hand came in to give food during his bad hours, Thomas would pounce, first at the food, then at the hand. After hearing a yelp, Thomas felt satisfaction wash over him, then feel ashamed and would apologize over and over again.

He eventually began to sense bugs in his head, just for a few seconds, and then they'd be gone, crawling out of his ears, into his water. Whenever Thomas felt them, he would count to three and if they were still there, he began yanking. Once a warm, gooey feeling trickled down his forehead he knew he killed the bugs, convinced it was their blood.

During the good hours, Thomas would think of his friends and how they would feel if they saw him like this. After some time, he would doze off, into a fitful, dreamless sleep.

 **A/N: So I know that most of this chapter was from the book but I figured it was the best method of introducing the plot. Thanks for reading so far! Sorry it was so short / I'll try to have the next chapter longer, and up by tomorrow.**


	2. The Visitor

**A/N: This chapter will be very gruesome and if you don't read it, it's ok, I'll do a summary of it in the end of this chapter. For everyone else, cheers!**

The 28th morning began like this. Thomas woke up feeling great and in control. After jogging for about 30 minutes, he lay back down with his whole body stretched out and concentrated to keep his mind as blank as possible. At some points he would feel a random feeling like despair or anger but Thomas would try hard to keep them down.

Then the food came, with a hand covered by a thick glove from past experiences, and shoved the metal tin at Thomas. He lost his concentration and looked up, grinning. Someone began giggling, which happened way to often and Thomas screamed at them yet again to shut it.

Grabbing his food, Thomas stuffed it in his mouth, missing most of it, which landed on the floor. The room, which had once been in a clean state, was littered with old food, water and glass. Thomas giggled, "Glass," he said aloud, "Funny, glaaaaass. Glasssssssss. GLASS!" Thomas grinned and shoved more food into his face.

He picked up the glass of water and gulped some down. _The_ _water_ _was_ _hard_ , _harder_ _than_ _usual_ , Thomas thought. Screwing up his face, he turned and threw the glass at the door filled with quick anger.

All of a sudden, a man appeared at the desk, scaring Thomas out of his wits, which he already had so few of. A hazy memory appeared in his head and he suddenly recognized the man. "Rat Man," Thomas spat, throwing all the hatred he could into those two words. "You dare come here? In my place? Get out! Get out get out GET OUT!"

The Rat Man only smirked which turned Thomas's fury into rage. He ran to the desk, ready to attack, but ran into a wall, the barrier.

Regaining some sense of control Thomas didn't attack again but hung his head. "What do you want?" He asked in a hoarse whisper, dropping to the floor.

The Rat Man took his opportunity and began to talk. "I have come to you for an important discussion we must have, one that you need to stay serious about, and not be... cranky." Rat Man smirked again, but Thomas, head still hanging, beckoned for him to continue. "This discussion involves the fate of your friends." Thomas looked up, surprised and angry.

"What did you do to them?" He demanded. At that, the Rat Man made a strangled sound that seemed like a laugh without the humor.

"Nothing for the moment, but what you decide might change that. You see, we've had a problem with the rest of the subjects, most aren't behaving or listening to us, like Newt, Minho or Siggy, as you know as Frypan." With the mention of his friends names, Thomas beamed. Of course they weren't following the directions, and thoughts of the glade flowed into his mind again. "We need a way to punish them," Rat Man continued. Thomas's head snapped up and he screamed "NO! Not them! Do the shuck whatever you want to me, but please, please don't harm them."

Standing up Thomas faced the man and got as close as he could to the desk and without planning what to do, began pounding his fist and kicking the barrier as hard as possible. Rat Man smirked again. "Oh, I hoped you would be unwilling," he sighed. "Listen, do that one more time and you will regret it." His calm, pleasant voice only fed dry wood to the already roaring fire burning Thomas's insides.

Ignoring him, Thomas backed up and charged the barrier but before he could reach it, a little spark of pain started in his back, stretching across his shoulder blades and to the front of the body. Thomas stifled a scream. But as quickly as it came, the electric agony stopped, leaving the upper half of Thomas's body throbbing and Thomas fell to the floor.

Grunting, he got up and began to scream at the top of his lungs, yelling incomprehensible words at Rat Man. The man just grinned again, impossiblely wider than before. The shock came, pinching at Thomas's insides, starting with his back and spreading up to his neck. Pain burst through Thomas's head and he soon felt the bugs come back. _Oh god, the bugs! Not the bugs_ "NOT THE BUGS!! GET THEM OUT OF MY HEAD YOU IDIOT! STOP THEM BEFORE THEY EAT ME!" The Rat Man began yelling in anger at the boy, which only made the crawling intensify.

Then, without warning, the insects crawled out of his head, leaving Thomas at peace. He soon got quiet and listened to the Rat Man yell. "Shut up you stupid boy!" With some control, Thomas raised his eyebrows at Rat Man. Rat Man took the hint. Heaving, he told Thomas cooly, "Listen to me kid, you either answer the question or your life will become a lot worse."

Thomas, who had seemed to gain some kind of calm control sat there. After about 3 minutes Rat Man spoke up, "Thomas," he spat, using the word like a dagger, "answer the damn question! Answer or terrible things will happen to you." Thomas didn't care what they did to him, as long as they didn't hurt his friends. Bloody faces of Newt, Minho and Teresa popped into his head but Thomas pushed them away.

Staring right into Rat Man's watery eyes, Thomas said, "I will not answer that. Do what you want to me but lay a finger on them and you will be a goner. Barier or not. Thomas crossed his arms but Rat Man just laughed. Thomas saw it before he felt it. The Rat Man grabbed a remote and pressed it, grinning maliciously.

Suddenly, unbearable pain shot through his entire body like he was being gunned down by rusty bullets. Some invisible force pressed him into a ball, forcing the pain to press in harder and harder, squeezing the air out. Thomas screamed like he never screamed before, all the hatred and pain and everything coming out. The flare didn't help, the bugs began crawling in, and Thomas was forced to arch his back further than it was meant to go, almost as if the bugs were controlling him.

Thomas screamed and screamed, blood drooling out the corners of his mouth. The agony tore him from his body, ripping him apart. Just as the pain began to die down, a fresh wave hit and Thomas couldn't even scream. Blood appeared at the corners of his mouth, nose, ears and eyes! His nails clawed at his legs, arms and head, trying to rid himself of the bugs.

Thomas found his voice again and began shrieking for help. But no one came. He was stuck in a room with a mad man. Thomas's body was jerked together, folding him as flat as possible. Muscles were being pulled, he felt things snapping. Just black out, he begged. Black out, please! Thomas got his wish, and black and white spots began dancing and covering his eyes.

Then the room vanished. But there was still pain. Floating in the darkness, Thomas's leg was the first to be felt. Screaming like all the pain that happened in his body was in his left leg, his head began to throb just as painfully. It was as if his eyes were being sunken into his skull, his toung being forced into his esophagus, his nose sliding down his face, his ears folding inward and forcing itself into his brain. And the hair. All the bugs had crawled right up to his head in the abnormal darkness in which he lay and Thomas thrashed and screamed. Pulling and tugging at his hair like before, but now going for his flesh. As his nails hit the fresh skin once again, there was pain, but the bugs crawled out and Thomas felt as though something left him.

He realized the pain was gone.

Waking up was as bad as the night before, except that dagger like throbs weren't stabbing him anymore, and the bugs had almost all been cleared out of his head.

With his eyes shut, Thomas lay still and tried to feel where the most damage was. At first, he believed it was his left leg. Then the torturously throbbing pain of his head, face and neck hit him again. Trying not to think, but just focus seemed like the way to go. It was almost as if a spikey metal ball had rolled its way up Thomas's neck and into his scull, coming out his eyes.

Attempting to keep his thoughts away, he imagined all darkness, except Teresa's face kept popping up, then Newt's, then Minho's, then Brenda's, Frypan's, Jorge's, and all the others. Even though Thomas couldn't smile on the outside, his heart was beaming. He missed them, and this time a different pain hit him, a pain of longing and sorrow for all the Gladers and others.

Still with his eyes closed, he mentally felt around for any other damage and relized that even though it still hurt, his right arm didn't seem to be in to much pain, more of an ache. He felt around and to his astonishment, no bones were broken. There was a huge amount of thick sticky stuff on his leg and neck though. After a moment, Thomas realized it was blood.

That's when the throw up came. He turned his head and began heaving and gagging. Soon after, he blacked out again.

Coming to, Thomas's mind felt blank. What had happened? Why was he on the floor, not in his corner? Why did the room smell like-Oh. Groaning, he actually attempted to open his eyes, but it was like they were glued together. Reaching his hand to his face took an eternity but Thomas managed.

There was a thin gooey crust on his eyelashes, preventing them to open. Thomas pulled some crust off and tore a few eyelashes as well. Grunting, he did that all along his right eye and soon he could open it.

Thomas was blinded by the light, shutting his eyes quickly, the white room was engraved into his eyelids. He covered his eye with the palm of his hand and a red light filtered through. This time, more slowly opening his eyes, he let them adjust to his palm, and slowly moving his palm away.

Squinting, Thomas found that he was laying flat in the middle of the small padded room. Repeating what he did with his right eye, he let his left eye adjust just as same. Letting himself stare at the ceiling seemed like the best idea, because he couldn't figure out how to get up. So far, Thomas had felt mostly in control, the pain waking him up, bringing him into reality.

After 15 minutes of lying and thinking, Thomas figured that he should get up, so pushing himself to the wall, he used his right arm to awkwardly heave himself up, using the floor and wall as his guide. Thomas's head was spinning like crazy and he slipped into unconsciousness once more.

 **A/N: I'm so sorry that had so much detail, but it will work with the plot. So if you did skip this chapter, here's a summary:**

 **Thomas spent his usual morning trying to keep himself from becoming a crank and after his food comes, Rat Man appears at the desk for the first time. Thomas charges the barrier screaming at him, then regains some kind of control and sits down. Rat Man explains that Thomas's friends haven't been behaving properly and he wants Thomas to deside a punishment for them. Thomas screams NO and charges the desk but before even hitting the barrier, pain sparks up his neck, making Thomas collapse to the floor. The pain stops and Thomas begins screaming jibberish at Rat Man. The pain spreads to his head and the rest of his body and Thomas feels the bugs crawl into his head. He yelps and Rat Man begins to yell as well. The bugs crawl out and Thomas stops. Thomas tells Rat Man to do all the harm to him, but not to touch any of his friends. Rat Man presses a button and Thomas is jerked forward, and then backwards, his body being forced to bend further than possible. Thomas blacks out but still feels the pain. Then the pain leaves with the bugs. Thomas wakes up and finds out that most of the pain is in his neck and left leg. He throws up and blacks out. Waking up, Thomas moves his hand and opens his eyes, realizing he's in the middle of the room. Thomas then tried to push his way up to lean against the wall but slips into unconsciousness once again.**

 **That's all! I'll try to get the next chapter up soon, hope you enjoyed!**


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